Dockerfile independent from debian package

Dockerfile

@@ -1,19 +1,73 @@
-#
-# From this base-image / starting-point
-#
-FROM debian:testing
+# Use a LTS Ubuntu version as parent image
+FROM ubuntu:16.04
+ARG DEBIAN_FRONTEND=noninteractive
+ARG PYTHONWARNINGS="ignore:Unverified HTTPS request"
+ENV LD_LIBRARY_PATH='/usr/local/lib'
+WORKDIR /opt
 
-#
-# Authorship
-#
-MAINTAINER ap13@sanger.ac.uk
+# Install general dependencies
+RUN apt-get update && apt-get install --no-install-recommends -y \
+ curl \
+ make \
+ automake \
+ gcc \
+ pkg-config \
+ zlib1g-dev \
+ autoconf \
+ check \
+ libtool \
+ libsubunit-dev \
+ git \
+ python3 \
+ python3-dev \
+ python3-setuptools \
+ python3-pip
 
-#
-# Pull in packages from testing
-#
-RUN apt-get update -qq
+# Install python dependencies 
+RUN pip3 install --trusted-host pypi.python.org --upgrade pip
+RUN pip3 install certifi \
+ && pip3 install wheel \
+ && pip3 install nose \
+ && pip3 install pillow \
+ && pip3 install dendropy \
+ && pip3 install biopython
+
+# Install RAxML
+ARG raxml_version='8.2.12'
+RUN curl -L https://github.com/stamatak/standard-RAxML/archive/v${raxml_version}.tar.gz -o standard-RAxML-${raxml_version}.tar.gz \
+ && tar xzf standard-RAxML-${raxml_version}.tar.gz \
+ && cd standard-RAxML-${raxml_version} \
+ && make -f Makefile.gcc \
+ && make -f Makefile.PTHREADS.gcc \
+ && cp raxmlHPC /usr/local/bin/ \
+ && cp raxmlHPC-PTHREADS /usr/local/bin/ \
+ && cd .. \
+ && rm -rf standard-RAxML-${raxml_version}
 
-#
-# Install Roary
-#
-RUN apt-get install -y gubbins
+# Install FastTree
+ARG fasttree_version='2.1.10'
+RUN curl http://www.microbesonline.org/fasttree/FastTree-${fasttree_version}.c -o FastTree.c \
+ && gcc -O3 -finline-functions -funroll-loops -Wall -o FastTree FastTree.c -lm \
+ && mv FastTree /usr/local/bin/ \
+ && rm FastTree.c
+
+# Install IQTree
+ARG iqtree_version='1.6.6'
+RUN curl -L https://github.com/Cibiv/IQ-TREE/releases/download/v${iqtree_version}/iqtree-${iqtree_version}-Linux.tar.gz -o iqtree-${iqtree_version}-Linux.tar.gz \
+ && tar xzf iqtree-${iqtree_version}-Linux.tar.gz \
+ && cp iqtree-${iqtree_version}-Linux/bin/iqtree /usr/local/bin \
+ && rm -rf iqtree-${iqtree_version}-Linux
+
+# Install Gubbins
+RUN git clone https://github.com/sanger-pathogens/gubbins.git \
+ && cd gubbins \
+ && autoreconf -i \
+ && ./configure \
+ && make \
+ && make check \
+ && make install \
+ && cd python \
+ && python3 setup.py install
+
+# Rename executable for backwards compatibility
+RUN mv /usr/local/bin/run_gubbins.py /usr/local/bin/run_gubbins

INSTALL.md

@@ -1,7 +1,7 @@
 Before you do anything, please have a look at the [Gubbins webpage](http://sanger-pathogens.github.io/gubbins/).
 
 # Installation
-There are a few ways to install Gubbins and its dependancies. The simpliest way is using conda.
+There are a few ways to install Gubbins and its dependencies. The simpliest way is using conda.
 
 * OSX/Linux - Bioconda
 * Linux - Ubuntu Xenial (16.04) & Debian (unstable)
@@ -22,42 +22,49 @@ conda install gubbins
 
 ## Linux - Ubuntu Xenial (16.04) & Debian (unstable)
 Gubbins has been packaged by the Debian Med team and is trivial to install using apt.
-```
-sudo apt-get install gubbins
-```
+
+ sudo apt-get install gubbins
 
 ## OSX/Linux/Cloud/Windows - Docker
 We have a docker container which gets automatically built from the latest version of Gubbins in Debian Med. To install it:
 
-```
-docker pull sangerpathogens/gubbins
-```
+ docker pull sangerpathogens/gubbins
+
+To use it you would use a command such as this:
+
+ docker run --rm -it -v <local_dir>:<remote_dir> sangerpathogens/gubbins run_gubbins -p <remote_dir>/<prefix> [<options>] <remote_dir>/<alignment_file>
+
+The flag `-v` synchronizes a directory on the host machine (here denoted as `<local_dir>`) with a directory in the Docker container (here denoted as `<remote_dir>`).
+`<remote_dir>` does not need to exist in the container before the run, a common choice is `/data`.
+Note that both `<local_dir>` and `<remote_dir>` must be absolute paths.
+
+The input alignment file must be present in `<local_dir>` (or in one of its subdirectories).
+In order to retrieve the files produced by Gubbins, run the program with option `-p`; 
+the argument of this option must consist of `<remote_dir>`, followed by an arbitrary identifier (here denoted as `<prefix>`).
 
-To use it you would use a command such as this (substituting in your directories), where your input files are assumed to be stored in /home/ubuntu/data:
-```
-docker run --rm -it -v /home/ubuntu/data:/data sangerpathogens/gubbins run_gubbins --help
-```
 
 ## OSX/Linux - from source
 This is the most difficult method and is only suitable for someone with advanced computing skills. Please consider using Conda instead.
 
-Install the dependances and include them in your PATH:
+Install the dependencies and include them in your `PATH`:
 * [FastTree](http://www.microbesonline.org/fasttree/#Install) ( >=2.1.4 )
 * [RAxML](https://github.com/stamatak/standard-RAxML) ( >=8.0 )
 * Python modules: Biopython (> 1.59), DendroPy (>=4.0), Reportlab, nose, pillow
 * Standard build environment tools (e.g. python3, pip3, make, autoconf, libtool, gcc, check, etc...)
 
+Clone or download the source code from GitHub and run the following commands to install Gubbins:
 ```
 autoreconf -i
-./configure
+./configure [--prefix=$PREFIX]
 make
-sudo make install
+[sudo] make install
 cd python
-sudo python3 setup.py install
+[sudo] python3 setup.py install
 ```
+Use `sudo` to install Gubbins system-wide. If you don't have the permissions, run `configure` with a prefix to install Gubbins in your home directory.
 
 ## OSX/Linux/Windows - Virtual Machine
-Roary wont run natively on Windows but we have created virtual machine which has all of the software setup, along with the test datasets from the paper. 
+Roary wont run natively on Windows but we have created a virtual machine which has all of the software setup, along with the test datasets from the paper. 
 It is based on [Bio-Linux 8](http://environmentalomics.org/bio-linux/). You need to first install [VirtualBox](https://www.virtualbox.org/), 
 then load the virtual machine, using the 'File -> Import Appliance' menu option. The root password is 'manager'.
 

VERSION

@@ -1 +1 @@
-2.3.2
+2.3.3